Researchers from VIB, KU Leuven, UGent, and Harvard report that they have succeeded in reconstructing DNA and proteins from prehistoric yeast cells. This made it possible to determine how genes developed and evolved into their current form over more than 100 million years.

“These results provide answers to an argument frequently used by opponents of the theory of evolution: the chance of the occurrence of a new characteristic, [i.e., a functional new segment of DNA] from scratch is similar to the chance of a modern jumbo jet assembling spontaneously from a few pieces of scrap metal,” said Kevin Verstrepen, from VIB/KU Leuven. “Many scientists have proposed that the new functional DNA does not appear out of thin air, but is built up gradually from a copy of an existing segment of functional DNA. By reconstructing a piece of prehistoric DNA that was copied several times during evolution, we were able to investigate the changes that occur in each of the copies and which gradually lead to new functions.”

An important unanswered question in Darwin’s theory of evolution is how new characteristics seem to appear out of nowhere. Such innovations appear to contradict the principle of gradual change, in which existing characteristics slowly evolve into another form. Yet scientists, who understand that many “inventions” took place during the evolution of life, do not know which processes form the basis of this evolutionary innovation.

One of the biggest problems is that virtually no prehistoric DNA sequences or proteins have been conserved, so that it is not possible to examine how these ancient versions differ from the current versions. This prevents the understanding of how new sections of DNA and new proteins developed.

Using a combination of the latest techniques in biology, the scientists Karin Voordeckers, Chris Brown, and Kevin Verstrepen from VIB in Leuven, together with Steven Maere (VIB/UGent), succeeded in rebuilding the DNA and proteins of prehistoric yeast cells.

“We used sequence reconstruction algorithms to predict the DNA sequence of ancestral genes from dozens of present-day DNA sequences,” explained Maere. “This enabled us to rebuild the corresponding ancestral proteins.”

According to Voordeckers, “We searched very specifically for how the yeast adapted to break down various sources of sugar. We found that the primal gene that codes for the protein for the digestion of maltose was copied a number of times during evolution. The DNA of some copies changed slightly, resulting in new proteins that could break down different sugars. By modeling these changes in the corresponding proteins, we now understand how just a few changes in the DNA can lead to the development of new activity in the corresponding proteins.”

The scientists think that this type of duplication of the DNA often forms the basis of the emergence of apparently new proteins. In other words, the jumbo jet is gradually built from a copy of an existing airplane. The research appears online today in PLoS Biology.

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